Shower – How long should thinset dry before gluing up tub surround

I would probably use unmodified thin set to cover the gaps and give a good base for applying the tile.

Could you do something a little decorative and use a border tile around the repaired area, sort of like a picture frame? Then use a different tile to fill in the area. The border would make the change in depth harder to see.

For a pure shower (not bathtub), I always put a membrane on over the backerboard. Redgard is my preferred choice right now so I would be fine with that choice.

I really don't think there is anything that you need to do. If I am putting plastic behind my backer I should see it sticking out under the backer and over the base in the picture - it would be covered by the lowest row of tile. It's not... not the biggest deal in the world if you have a membrane plus backer.

Final take: There is nothing wrong with Zhentar's advice. If I were doing a bath/shower combo it is exactly what I would say. However with the use of caulking for all of the gaps I would one a solid membrane over the area. The fact is the caulk will dry out expand/contract and may leak after 5 years or so. You are binding the caulk to larger materials like the DS which will have different expansion rates. With a membrane you have one solid surface that is made not to crack.